The document, which states that research on animals is currently "essential", sets out new restrictions on the use of monkeys and includes some species of primitive fish and invertebrates, such as crabs and lobsters, that were not previously covered by European legislation.

According to the proposed new directive: "The use of animals in scientific procedures today ... still remains essential for ensuring a level of safety for human beings, animals and the environment and for the advancement of knowledge which will lead to improvements in human and animal health and welfare."

However, the European environment commissioner Stavros Dimas said: "It is absolutely important to steer away from testing on animals. Scientific research must focus on finding alternative methods to animal testing, but where alternatives are not available the situation of animals still used in experiments must be improved."

Scientists had been concerned that the commission's proposals, which if adopted by the EU would replace 1986 legislation, placing far greater restrictions on animal experimentation and imposing extra bureaucracy.

On October 24, Chris Brinsmead, president of the Association of the British Pharmaceutical Industry, Simon Denegri, chief executive of the Association of Medical Research Charities, and Prof Dame Nancy Rotherwell, president of the Biosciences Federation, wrote a letter raising their concerns to the Home Secretary Jacqui Smith and other ministers including Lord Mandelson and Hilary Benn.

With that letter was a briefing document produced by a group of scientific organisations, including the Royal Society and the Academy of Medical Sciences, which stated: "The sector is concerned at some of the proposals that have been raised in public documents and in discussions with officials."

The letter proposed the creation of a "pan-government task force" to coordinate lobbying of the commission.

Whether as a result of UK government lobbying or not, the final proposal will be much more palatable to the scientific community. "It has been improved considerably so that it is much more realistic," said Dr Simon Festing, director of the Research Defence Society. "It really is a very good first stab."

Most eye-catching is the ban on the use of great apes – which scientists had opposed in their letter to the Home Secretary. They wrote: "Should a serious health challenge arise where great apes offer the only option to address a pandemic that threatens widespread mortality, their use should be permitted ... but this would not be possible if a complete legislative ban were introduced."

In effect, such a ban would make little difference, though, because no great apes have been used in research in the EU for the past six years and UK regulations forbid their use.

Although retaining the idea of a legislative ban, the proposed directive does offer a "safeguard clause" that allows chimps, gorillas and orang-utans to be used under exceptional circumstances if a member state applies for permission from the commission.

But this could take too long in a public health emergency, argues Dr Sophie Petit-Zeman at the Association of Medical Research Charities. "A ban on the use of great apes ... could jeopardise rapid reactive work to a serious health challenge," she said.

Researchers had been concerned that proposals would include a ban on the use of non-human primates that are either the progeny or grand-progeny of wild animals. This proposal was aimed at promoting long-term captive breeding as an alternative to capturing animals in the wild.

"The capture of non-human primates from the wild is highly stressful for the animals and increases the risk of injury and suffering during capture and transport," states the proposed directive.

But researchers had pointed out that it would be impossible to meet the demand for animals in the short term if the progeny of individuals caught in the wild were excluded, and the final document has allowed such a ban to be phased in over 7 or 10 years depending on the species of monkey.

Emily McIvor, policy director of the Dr Hadwen Trust, an NGO that campaigns against the use of animals in research, gave a cautious welcome to the proposals.

But she added: "To make this law fit for a morally and scientifically progressive 21st century, the ultimate goal of replacing animals with alternatives must be right at the heart of the legislation. This is a once-in-a-lifetime opportunity for Europe to lead the world in ending animal experiments and replacing them with the most technologically advanced non-animal techniques science can offer."